Guarnier (Boels Dolmans) came in first in the 124 kilometres sprint stage around Torre del Greco with Olympic champion Van der Breggen among the group contesting the finish.
Amanda Spratt (Orica-Scott) and Katarzyna Niewiadoma (WM3 Pro Cycling) came in second and third respectively in the final stage.
Italy's Elisa Longo Borghini (Wiggle High5) finished second in the general classification, one minute three seconds behind Van der Breggen, with Annemiek van Vleuten (Orica-Scott) third.
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The stage featured nine laps of 11.1km before a detour up Mount Vesuvio on a final lap.
A breakaway group was caught heading up Vesuvio before a group of six, including pink jersey-holder Van der Breggen and Guarnier, pushed for victory.
Van Vleuten and Van der Breggen both attacked but it was Guarnier who eventually prevailed in a tight finish.
Van der Breggen's race victory also saw her reclaim the Women's World Tour's purple jersey.
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